GensearchNGS

GensearchNGS is an integrated software solution for the analysis of DNA-Seq data from commonly used NGS equipments such as Illumina, Ion Torrent, Roche/454, and Proton. It has been designed and developed in close collaboration with leading accredited diagnostics groups in Europe and with the support of the NMDchip FP7 project. GensearchNGS is used in many diagnostics and research laboratories across Europe, on human genome, as well as certain viral, bacterial and plant genomes. It requires no bio-informatics training.

Screen shots:

GensearchNGS screenshot 1 GensearchNGS screenshot 2 GensearchNGS screenshot 3 GensearchNGS screenshot 4 GensearchNGS screenshot 5

It integrates all the steps from importing and filtering sequence reads, bar code splitting, alignment, variant detection and annotation to the final report of detected variants. Variants can be annotated with various public and private data sources (Ensembl, Alamut, NCBI,...) They can be filtered by logical combinations between samples for family studies.

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Main features:

  • User friendly software for resequencing NGS projects in a diagnostic setting, running on Windows, Linux and MacOS systems.
  • Connects to variant interpretation tools, and databases such as: Ensembl, dbSNP, Alamut, Clinvar, Wiki Pathways,Gene Ontology.
  • Filter variants across samples (e.g. variants common to several samples or exclude variants of one sample from another).
  • Patient centric database system to manage sequence data and validated variants.
  • Customisation possible to export data into your laboratory management system.
  • Possibility to publish your variants on Clinvar.
  • Developed together with accredited laboratories.
  • For larger projects (WES/WGS): possibility to use multiple PCs in parallel.
  • Plugin technology: alignment with our proprietary or public algorithms such as Bowtie, BWA or Stampy.
  • Annotation and filtering with HPO, OMIM and Orphanet descriptors and codes, helpful when fishing for mutations in whole exomes or whole genomes.
  • Tools to analyse coverage and detect CNV*).
  • Tools to analyse trios and more samples from the same family*).
  • Sanger validation step: you can attach to patients in the database and visualise amplicons sequenced with a capillary sequencer to validate that the NGS detected variant is indeed not an artefact.
  • Various features related to SARS-CoV2 analysis, see our application note.
  • RNAseq and DNAmeth data analysis*).

Did we wake your interest? You can download a limited demo version after registration. This will allow you to access the download area in our products section.

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Some publications, posters and references:

Peritoneal or mesenteric tumours revealing histiocytosis
Authors: Cohen- Aubart F, Ungureanu I, Razanamahery J, et al.
Publication: BMJ Open Gastro 2021;8:e000622. doi:10.1136/bmjgast-2021-000622

Report of two siblings with spondylodysplastic Ehlers-Danlos syndrome and B4GALT7 deficiency
Authors: Lorenz, D., Kress, W., Zaum, AK. et al.
Publication: BMC Pediatr 21, 293 (2021)

Genetic analysis of sudden unexpected death cases: Evaluation of library preparation methods to handle heterogeneous sample material
Authors: Stefanie Scheiper-Welling, Stephanie Körberb, Christof Geisen, Marcel A.Verhoff, Silke Kauferstein
Publication: Forensic Science International, Volume 322,2021,110768,ISSN 0379-0738, https://doi.org/10.1016/j.forsciint.2021.110768.

Post-mortem genetic investigation of cardiac disease–associated genes in sudden infant death syndrome (SIDS) cases
Authors: Jasmin Köffer, Stefanie Scheiper-Welling, Marcel A. Verhoff, Thomas Bajanowski & Silke Kauferstein
Publication: Int J Legal Med 135, 207–212 (2021). https://doi.org/10.1007/s00414-020-02394-x

Quantifying sequencing error and effective sequencing depth of liquid biopsy NGS with UMI error correction
Authors: Malene Støchkel Frank, Janina Fuß, Tim Alexander Steiert, Greta Streleckiene, Julie Gehl & Michael Forster
Publication: BIOTECHNIQUES AHEAD OF PRINT BENCHMARK Published Online:29 Jan 2021. doi:10.2144/btn-2020-0124

Characterization of an N-terminal Nav1.5 channel variant – a potential risk factor for arrhythmias and sudden death?
Authors: Stefanie Scheiper-Welling, Paolo Zuccolini, Oliver Rauh, Britt-Maria Beckmann, Christof Geisen, Anna Moroni, Gerhard Thiel & Silke Kauferstein
Publication: BMC Medical Genetics volume 21, Article number: 227 (2020)

A novel missense variant in MYO3A is associated with autosomal dominant high‐frequency hearing loss in a German family
Authors: Julia Doll, Michaela A. H. Hofrichter, Paulina Bahena, Alfred Heihoff, Dennis Segebarth, Tobias Müller, Marcus Dittrich, Thomas Haaf, Barbara Vona
Publication: Mol Genet Genomic Med. 2020;8:e1343. https://doi.org/10.1002/mgg3.1343

New Insights on Genetic Diagnostics in Cardiomyopathy and Arrhythmia Patients Gained by Stepwise Exome Data Analysis
Authors: Konstantinos Kolokotronis, Natalie Pluta, Eva Klopocki, Erdmute Kunstmann, Daniel Messroghli, Christoph Maack, Shai Tejman-Yarden, Michael Arad, Simone Rost and Brenda Gerull
Publication: J. Clin. Med. 2020, 9(7), 2168; https://doi.org/10.3390/jcm9072168

Intratumor heterogeneity of prognostic DNA-based molecular markers in adrenocortical carcinoma
Authors: Anne Jouinot, Juliane Lippert, Martin Fassnacht, Bruno de La Villeon, Amandine Septier, Mario Neou1, Karine Perlemoine1, Silke Appenzeller, Mathilde Sibony, Sébastien Gaujoux1,6, Bertrand Dousset, Rossella Libe, Lionel Groussin, Cristina L Ronchi, Guillaume Assié, and Jérôme Bertherat
Publication: Endocrine Connections(2020)9,705–714

Genetic Spectrum of Syndromic and Non-Syndromic Hearing Loss in Pakistani Families.
Authors:Julia Doll, Barbara Vona,Linda Schnapp, Franz Rüschendorf, Imran Khan, Saadullah Khan, Noor Muhammad, Sher Alam Khan, Hamed Nawaz, Ajmal Khan, Naseer Ahmad, Susanne M. Kolb, Laura Kühlewein, Jonathan D. J. Labonne, Lawrence C. Layman, Michaela A. H. Hofrichter, Tabea Röder, Marcus Dittrich, Tobias Müller, Tyler D. Graves, Il-Keun Kong, Indrajit Nanda, Hyung-Goo Kim, Thomas Haaf
Publication: Genes 2020, 11(11), 1329; https://doi.org/10.3390/genes11111329

Biallelic TANGO1 mutations cause a novel syndromal disease due to hampered cellular collagen secretion.
Authors: Caroline Lekszas, Ombretta Foresti, Ishier Raote, Daniel Liedtke, Eva-Maria König, Indrajit Nanda, Barbara Vona, Peter De Coster, Rita Cauwels, Vivek Malhotra, Thomas Haaf
Publication: eLife 2020;9:e51319 DOI: 10.7554/eLife.51319

Rapid response of stage IV colorectal cancer with APC/TP53/KRAS mutations to FOLFIRI and Bevacizumab combination chemotherapy: a case report of use of liquid biopsy.
Authors: Hendricks A, Rosenstiel P, Hinz S, Burmeister G, Röcken C, Boersch K, Schafmayer C, Becker T, Franke A, Forster M.
Publication: BMC Med Genet. 2020 Jan 3;21(1):3. doi: 10.1186/s12881-019-0941-5.

A comprehensive method protocol for annotation and integrated functional understanding of lncRNAs.
Authors: Meik Kunz, Beat Wolf, Maximilian Fuchs, Jan Christoph, Ke Xiao, Thomas Thum, David Atlan, Hans-Ulrich Prokosch, Thomas Dandekar
Publication: Briefings in Bioinformatics, Volume 21, Issue 4, July 2020, Pages 1391–1396, https://doi.org/10.1093/bib/bbz066

The Alazami Syndrome-Associated Protein LARP7 Guides U6 Small Nuclear RNA Modification and Contributes to Splicing Robustness
Authors: Daniele Hasler, Rajyalakshmi Meduri, Maciej Bąk, Gerhard Lehmann, Leonhard Heizinger, Xin Wang, Zhi-Tong Li, François M.Sement, Astrid Bruckmann, Anne-Catherine Dock-Bregeon, Rainer Merkl, Reinhard Kalb, Eva Grauer, Erdmute Kunstmann, Mihaela Zavolan, Mo-Fang Liu, Utz Fischer, Gunter Meister
Publication: Molecular Cell Volume 77, Issue 5, 5 March 2020, Pages 1014-1031.e13

Use of Targeted High-Throughput Sequencing for Genetic Classification of Patients with Bleeding Diathesis and Suspected Platelet Disorder.
Authors: Oliver Andres,Eva-Maria König,Karina Althaus,Tamam Bakchoul,Peter Bugert,Stefan Eber,Ralf Knöfler,Erdmute Kunstmann, Georgi Manukjan, Oliver Meyer, Gabriele Strauß, Werner Streif, Thomas Thiele, Verena Wiegering, Eva Klopocki, Harald Schulze, on Behalf of the THROMKIDplus Study Group of the Society of Paediatric Oncology Haematology (Gesellschaft für Pädiatrische Onkologie und Hämatologie, GPOH) and the Society of Thrombosis Haemostasis Research (Gesellschaft für Thrombose- und Hämostaseforschung, GTH)
Publication: CC BY 4.0 · TH Open 2018; 02(04): e445-e454

Single CpG hypermethylation, allele methylation errors, and decreased expression of multiple tumor suppressor genes in normal body cells of mutation-negative early-onset and high-risk breast cancer patients.
Authors: Böck J, Appenzeller S, Haertle L, Schneider T, Gehrig A, Schröder J, Rost S, Wolf B, Bartram CR, Sutter C, Haaf T
Publication: Int J Cancer. 2018 Apr 16. doi: 10.1002/ijc.31526. [Epub ahead of print]

Non-Coding RNAs in Lung Cancer: Contribution of Bioinformatics Analysis to the Development of Non-Invasive Diagnostic Tools.
Authors: Meik Kunz, Beat Wolf, Harald Schulze, David Atlan, Thorsten Walles, Heike Walles, and Thomas Dandekar
Publication: Genes (Basel). 2017 Jan; 8(1): 8. Published online 2016 Dec 26. doi: 10.3390/genes8010008

A Novel de novo Mutation in CEACAM16 Associated with Postlingual Hearing Impairment.
Authors: Michaela A.H. Hofrichter, Indrajit Nanda, Jens Gräf, Jörg Schröder, Wafaa Shehata-Dieler, Barbara Vona, Thomas Haaf
Publication: Molecular syndromology 6(4) · August 2015 | DOI: 10.1159/000439576

Research Article DNAseq Workflow in a Diagnostic Context and an Example of a User Friendly Implementation.
Authors: Wolf, B., Kuonen, P., Dandekar, Th., Atlan, D.
Publication: BioMed Research International 2015 · June 2015 | DOI: 10.1155/2015/403497

Nail–Patella Syndrome: clinical and molecular data in 55 families raising the hypothesis of a genetic heterogeneity.
Authors: Ghoumid, J., Petit, F., Holder-Espinasse, M., Jourdain, A. S., Guerra, J., Dieux-Coeslier, A., ... & Escande, F.
Publication: European Journal of Human Genetics , (22 April 2015) | doi:10.1038/ejhg.2015.77

Analysis of circulating cell free DNA (ccfDNA): A promising tool for personalized medicine and cancer therapy
Authors: Keup C., Mardin W., Dworniczak J., Dockhorn B., Rijcken E., Dworniczak B.
Conference: GfH Jahrestagung, 2015

Identification of deep intronic variants in 15 haemophilia A patients by next generation sequencing of the whole factor VIII gene.
Authors: Bach JE, Wolf B, Oldenburg J, Müller CR, Rost S.
Publication: European Journal of Human Genetics , (5 November 2014) | Thromb Haemost. 2015 May 7;114(3).

Zur genetischen Heterogenität der Muskeldystrophien : alternative genetische Ursachen der Myotonen Dystrophie und FSHD.
Author: Mirjam Larsen
Publication: Doctoral thesis, University of Würzburg · December 2015

Distal hereditary motor neuropathy due to BSCL2 mutation in a two generation family
Authors: Ann-Kathrin Zaum, Simone Rost, Beat Wolf, Clemens R. Müller, Thomas Musacchio, Erdmute Kunstmann, Stephan Klebe
Conference: GfH Jahrestagung, 2015

Hereditary Breast/Ovarian Cancer: A systematic screening of DNA repair genes in 300 consecutive patients
Authors: Andrea Gehrig, Birgit Halliger-Keller, Clemens R. Müller
Conference: GfH Jahrestagung, 2015

Novel compound heterozygous mutations in PLEC1 causing epidermolysis bullosa simplex with muscular dystrophy
Authors: Simone Rost, Ann-Kathrin Zaum, Andrea Gehrig, Birgit Halliger-Keller, Wolfram Kress, Clemens R. Müller, Mathias Buttmann, Erdmute Kunstmann
Conference: GfH Jahrestagung, 2015

Deep intronic variants in the factor VIII gene
Authors: J Elisa Bach, Beat Wolf, Johannes Oldenburg, Clemens R Müller, Simone Rost
Conference: GfH Jahrestagung, 2015

Next-generation DNA sequencing of a Swedish malignant hyperthermia cohort
Authors: M. Broman, I. Kleinschnitz, J.E. Bach, S. Rost, G. Islander and C.R. Müller
 Publication: Clinical Genetics  | doi:10.1111/cge.12508

Analysis of circulating cell free DNA (ccfDNA): A promising tool for personalized medicine and cancer therapy
Authors: Keup C., Mardin W., Dworniczak J., Dockhorn B., Haier J., Rijcken E., Rijcken E., Dworniczak B.
Conference: 13th International Symposium on Mutation in the Genome: detection, genome sequencing & interpretation

Diagnostic approach for FSHD revisited: SMCHD1 mutations cause FSHD2 and act as modifiers of disease severity in FSHD1
Authors: Mirjam Larsen, Simone Rost, Nady El Hajj, Andreas Ferbert, Marcus Deschauer, Maggie C Walter, Benedikt Schoser, Pawel Tacik, Wolfram Kress and Clemens R Müller
Publication: European Journal of Human Genetics , (5 November 2014) | doi:10.1038/ejhg.2014.191

VHL mosaicism can be detected by clinical next-generation sequencing and is not restricted to patients with a mild phenotype.
Authors: Lucie Coppin, Claudine Grutzmacher, Michel Crépin, Evelyne Destailleur, Sophie Giraud, Catherine Cardot-Bauters, Nicole Porchet and Pascal Pigny
Publication: European Journal of Human Genetics, 2014, vol. 22, no 9, p. 1149-1152.

Unusual multisystemic involvement and a novel BAG3 mutation revealed by NGS screening in a large cohort of myofibrillar myopathies
Authors: Anna-Lena Semmler et al.
Publication: Orphanet Journal of Rare Diseases 2014, 9:121 doi:10.1186/s13023-014-0121-9

NGS panel for diagnostics of myofibrillar myopathies
Authors: J Elisa Bach, Simone Rost, Anna-Lena Semmler, Kristl G Claeys, Beat Wolf, Wolfram Kress, Clemens R Müller
Conference: GfH Jahrestagung, 2014

A novel approach for heuristic pairwise DNA sequence alignment
Authors: Beat Wolf, Pierre Kuonen
Conference: BIOCOMP'13 - The 2013 International Conference on Bioinformatics & Computational Biology

Novel form of X-linked nonsyndromic hearing loss with cochlear malformation caused by a mutation in the type IV collagen gene COL4A6
Authors: Simone Rost, Elisa Bach, Cordula Neuner, Indrajit Nanda, Sandra Dysek, Reginald E Bittner,
Alexander Keller, Oliver Bartsch, Robert Mlynski, Thomas Haaf, Clemens R Muller and Erdmute Kunstmann.
European Journal of Human Genetics advance online publication 29 May 2013; doi: 10.1038/ejhg.2013.108

IonTorrent: high throughput sequencing in a diagnostic laboratory
Authors: B. Dworniczak, S. Fleige-Menzen, P. Pennekamp.
Conference: European Human Genetics Conference 2013

Store, align and explore your genome outside the Cloud, at home, on your PC
Authors: P. Kuonen, B. Wolf, JT den Dunnen, D.Atlan, T. Dandekar
Conference: European Human Genetics Conference 2013

Nail-Patella Syndrome: evidence for genetic heterogeneity (Poster 01.021)
Authors: F. Petit, F. Escande, A. Jourdain, C. Baumann, F. Fellmann, D. Lacombe, S. Marlin, S. Odent, N. Porchet, M. Holder-Espinasse, S. Manouvrier-Hanu
Conference: European Human Genetics Conference 2013

Novel form of X-linked nonsyndromic hearing loss caused by a mutation in a type IV collagen gene (Poster P-MonoG-202)
Authors: Rost, Bach, Neuner, Nanda, Dysek, Bittner, Keller, Bartsch O., Mlynski, Haaf, Müller, Kunstmann
Conference: GfH Jahrestagung, 2013

Application of targeted next-generation sequencing for molecular diagnostics of Malignant Hyperthermia and Central Core Disease (Poster P-ClinG-087)
Authors: Kleinschnitz I., Bach J.E., Rost S., Gehrig A., Müller C.R.
Conference: GfH Jahrestagung, 2013

NGS goes diagnostics: Multiplex analysis of genes for limb-girdle muscular dystrophies (Poster P-ClinG-045)
Authors: Bach J.E., Rost S., Gehrig A., Kress W., Müller C.R.
Conference: GfH Jahrestagung, 2013

Screening of muscular disease genes with the Access Array System of Fluidigm and Roche’s GS Junior
Authors: J. E. Bach, S. Rost, A. Gehrig, C. R. Müller
Conference: European Human Genetics Conference 2012

IonTorrent: 2nd generation sequencing in a diagnostic laboratory 
Authors: B. Dworniczak, S. Fleige-Menzen, N. Bogdanova-Markov, P. Pennekamp
Conference: European Human Genetics Conference 2012

*) under development.

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